OBJECTIVE: Aortic dissection (AD) is a serious condition requiring rapid and accurate diagnosis. In this study, we aimed to improve the diagnostic accuracy of AD by presenting a novel method for aortic segmentation in computed tomography images that uses a combination of a transformer and a UNet cascade network with a Zoom-Out and Zoom-In scheme (ZOZI-seg).
METHODS: The proposed method segments each compartment of the aorta, comprising the true lumen (TL), false lumen (FL), and thrombosis (TH) using a cascade strategy that captures both the global context (anatomical structure) and the local detail texture based on the dynamic patch size with ZOZI schemes. The ZOZI-seg model has a two-stage architecture using both a \"3D transformer for panoptic context-awareness\" and a \"3D UNet for localized texture refinement.\" The unique ZOZI strategies for patching were demonstrated in an ablation study. The performance of our proposed ZOZI-seg model was tested using a dataset from Asan Medical Center and compared with those of existing models such as nnUNet and nnFormer.
RESULTS: In terms of segmentation accuracy, our method yielded better results, with Dice similarity coefficients (DSCs) of 0.917, 0.882, and 0.630 for TL, FL, and TH, respectively. Furthermore, we indirectly compared our model with those in previous studies using an external dataset to evaluate its robustness and generalizability.
CONCLUSIONS: This approach may help in the diagnosis and treatment of AD in different clinical situations and provide a strong basis for further research and clinical applications.

UNASSIGNED: Automatic segmentation of corneal stromal cells can assist ophthalmologists to detect abnormal morphology in confocal microscopy images, thereby assessing the virus infection or conical mutation of corneas, and avoiding irreversible pathological damage. However, the corneal stromal cells often suffer from uneven illumination and disordered vascular occlusion, resulting in inaccurate segmentation.
UNASSIGNED: In response to these challenges, this study proposes a novel approach: a nnUNet and nested Transformer-based network integrated with dual high-order channel attention, named U-NTCA. Unlike nnUNet, this architecture allows for the recursive transmission of crucial contextual features and direct interaction of features across layers to improve the accuracy of cell recognition in low-quality regions. The proposed methodology involves multiple steps. Firstly, three underlying features with the same channel number are sent into an attention channel named gnConv to facilitate higher-order interaction of local context. Secondly, we leverage different layers in U-Net to integrate Transformer nested with gnConv, and concatenate multiple Transformers to transmit multi-scale features in a bottom-up manner. We encode the downsampling features, corresponding upsampling features, and low-level feature information transmitted from lower layers to model potential correlations between features of varying sizes and resolutions. These multi-scale features play a pivotal role in refining the position information and morphological details of the current layer through recursive transmission.
UNASSIGNED: Experimental results on a clinical dataset including 136 images show that the proposed method achieves competitive performance with a Dice score of 82.72% and an AUC (Area Under Curve) of 90.92%, which are higher than the performance of nnUNet.
UNASSIGNED: The experimental results indicate that our model provides a cost-effective and high-precision segmentation solution for corneal stromal cells, particularly in challenging image scenarios.

Three-dimensional (3D) ultrasound can assess the margins of resected tongue carcinoma during surgery. Manual segmentation (MS) is time-consuming, labour-intensive, and subject to operator variability. This study aims to investigate use of a 3D deep learning model for fast intraoperative segmentation of tongue carcinoma in 3D ultrasound volumes. Additionally, it investigates the clinical effect of automatic segmentation. A 3D No New U-Net (nnUNet) was trained on 113 manually annotated ultrasound volumes of resected tongue carcinoma. The model was implemented on a mobile workstation and clinically validated on 16 prospectively included tongue carcinoma patients. Different prediction settings were investigated. Automatic segmentations with multiple islands were adjusted by selecting the best-representing island. The final margin status (FMS) based on automatic, semi-automatic, and manual segmentation was computed and compared with the histopathological margin. The standard 3D nnUNet resulted in the best-performing automatic segmentation with a mean (SD) Dice volumetric score of 0.65 (0.30), Dice surface score of 0.73 (0.26), average surface distance of 0.44 (0.61) mm, Hausdorff distance of 6.65 (8.84) mm, and prediction time of 8 seconds. FMS based on automatic segmentation had a low correlation with histopathology (r = 0.12, p = 0.67); MS resulted in a moderate but insignificant correlation with histopathology (r = 0.4, p = 0.12, n = 16). Implementing the 3D nnUNet yielded fast, automatic segmentation of tongue carcinoma in 3D ultrasound volumes. Correlation between FMS and histopathology obtained from these segmentations was lower than the moderate correlation between MS and histopathology.

UNASSIGNED: Linear accelerator (linac) incorporating a magnetic resonance (MR) imaging device providing enhanced soft tissue contrast is particularly suited for abdominal radiation therapy. In particular, accurate segmentation for abdominal tumors and organs at risk (OARs) required for the treatment planning is becoming possible. Currently, this segmentation is performed manually by radiation oncologists. This process is very time consuming and subject to inter and intra operator variabilities. In this work, deep learning based automatic segmentation solutions were investigated for abdominal OARs on 0.35 T MR-images.
UNASSIGNED: One hundred and twenty one sets of abdominal MR images and their corresponding ground truth segmentations were collected and used for this work. The OARs of interest included the liver, the kidneys, the spinal cord, the stomach and the duodenum. Several UNet based models have been trained in 2D (the Classical UNet, the ResAttention UNet, the EfficientNet UNet, and the nnUNet). The best model was then trained with a 3D strategy in order to investigate possible improvements. Geometrical metrics such as Dice Similarity Coefficient (DSC), Intersection over Union (IoU), Hausdorff Distance (HD) and analysis of the calculated volumes (thanks to Bland-Altman plot) were performed to evaluate the results.
UNASSIGNED: The nnUNet trained in 3D mode achieved the best performance, with DSC scores for the liver, the kidneys, the spinal cord, the stomach, and the duodenum of 0.96 ± 0.01, 0.91 ± 0.02, 0.91 ± 0.01, 0.83 ± 0.10, and 0.69 ± 0.15, respectively. The matching IoU scores were 0.92 ± 0.01, 0.84 ± 0.04, 0.84 ± 0.02, 0.54 ± 0.16 and 0.72 ± 0.13. The corresponding HD scores were 13.0 ± 6.0 mm, 16.0 ± 6.6 mm, 3.3 ± 0.7 mm, 35.0 ± 33.0 mm, and 42.0 ± 24.0 mm. The analysis of the calculated volumes followed the same behavior.
UNASSIGNED: Although the segmentation results for the duodenum were not optimal, these findings imply a potential clinical application of the 3D nnUNet model for the segmentation of abdominal OARs for images from 0.35 T MR-Linac.

Objective. Both local and global context information is crucial semantic features for brain tumor segmentation, while almost all the CNN-based methods cannot learn global spatial dependencies very well due to the limitation of convolution operations. The purpose of this paper is to build a new framework to make full use of local and global features from multimodal MR images for improving the performance of brain tumor segmentation.Approach. A new automated segmentation method named nnUnetFormer was proposed based on nnUnet and transformer. It fused transformer modules into the deeper layers of the nnUnet framework to efficiently obtain both local and global features of lesion regions from multimodal MR images.Main results.We evaluated our method on BraTS 2021 dataset by 5-fold cross-validation and achieved excellent performance with Dice similarity coefficient (DSC) 0.936, 0.921 and 0.872, and 95th percentile of Hausdorff distance (HD95) 3.96, 4.57 and 10.45 for the regions of whole tumor (WT), tumor core (TC), and enhancing tumor (ET), respectively, which outperformed recent state-of-the-art methods in terms of both average DSC and average HD95. Besides, ablation experiments showed that fusing transformer into our modified nnUnet framework improves the performance of brain tumor segmentation, especially for the TC region. Moreover, for validating the generalization capacity of our method, we further conducted experiments on FeTS 2021 dataset and achieved satisfactory segmentation performance on 11 unseen institutions with DSC 0.912, 0.872 and 0.759, and HD95 6.16, 8.81 and 38.50 for the regions of WT, TC, and ET, respectively.Significance. Extensive qualitative and quantitative experimental results demonstrated that the proposed method has competitive performance against the state-of-the-art methods, indicating its interest for clinical applications.

UNASSIGNED: Artificial intelligence (AI)-automated tumor delineation for pediatric gliomas would enable real-time volumetric evaluation to support diagnosis, treatment response assessment, and clinical decision-making. Auto-segmentation algorithms for pediatric tumors are rare, due to limited data availability, and algorithms have yet to demonstrate clinical translation.
UNASSIGNED: We leveraged two datasets from a national brain tumor consortium (n=184) and a pediatric cancer center (n=100) to develop, externally validate, and clinically benchmark deep learning neural networks for pediatric low-grade glioma (pLGG) segmentation using a novel in-domain, stepwise transfer learning approach. The best model [via Dice similarity coefficient (DSC)] was externally validated and subject to randomized, blinded evaluation by three expert clinicians wherein clinicians assessed clinical acceptability of expert- and AI-generated segmentations via 10-point Likert scales and Turing tests.
UNASSIGNED: The best AI model utilized in-domain, stepwise transfer learning (median DSC: 0.877 [IQR 0.715-0.914]) versus baseline model (median DSC 0.812 [IQR 0.559-0.888]; p<0.05). On external testing (n=60), the AI model yielded accuracy comparable to inter-expert agreement (median DSC: 0.834 [IQR 0.726-0.901] vs. 0.861 [IQR 0.795-0.905], p=0.13). On clinical benchmarking (n=100 scans, 300 segmentations from 3 experts), the experts rated the AI model higher on average compared to other experts (median Likert rating: 9 [IQR 7-9]) vs. 7 [IQR 7-9], p<0.05 for each). Additionally, the AI segmentations had significantly higher (p<0.05) overall acceptability compared to experts on average (80.2% vs. 65.4%). Experts correctly predicted the origins of AI segmentations in an average of 26.0% of cases.
UNASSIGNED: Stepwise transfer learning enabled expert-level, automated pediatric brain tumor auto-segmentation and volumetric measurement with a high level of clinical acceptability. This approach may enable development and translation of AI imaging segmentation algorithms in limited data scenarios.

OBJECTIVE: Neuroendocrine tumors (NETs) are a rare form of cancer that can occur anywhere in the body and commonly metastasizes. The large variance in location and aggressiveness of the tumors makes it a difficult cancer to treat. Assessments of the whole-body tumor burden in a patient image allow for better tracking of disease progression and inform better treatment decisions. Currently, radiologists rely on qualitative assessments of this metric since manual segmentation is unfeasible within a typical busy clinical workflow.
METHODS: We address these challenges by extending the application of the nnU-net pipeline to produce automatic NET segmentation models. We utilize the ideal imaging type of 68Ga-DOTATATE PET/CT to produce segmentation masks from which to calculate total tumor burden metrics. We provide a human-level baseline for the task and perform ablation experiments of model inputs, architectures, and loss functions.
RESULTS: Our dataset is comprised of 915 PET/CT scans and is divided into a held-out test set (87 cases) and 5 training subsets to perform cross-validation. The proposed models achieve test Dice scores of 0.644, on par with our inter-annotator Dice score on a subset 6 patients of 0.682. If we apply our modified Dice score to the predictions, the test performance reaches a score of 0.80.
CONCLUSIONS: In this paper, we demonstrate the ability to automatically generate accurate NET segmentation masks given PET images through supervised learning. We publish the model for extended use and to support the treatment planning of this rare cancer.

BACKGROUND: Endovascular thrombectomy (EVT) duration is an important predictor for neurological outcome. Recently it was shown that an angle of ≤ 90° of the internal carotid artery (ICA) is predictive for longer EVT duration. As manual angle measurement is not trivial and time-consuming, deep learning (DL) could help identifying difficult EVT cases in advance.
METHODS: We included 379 CT angiographies (CTA) of patients who underwent EVT between January 2016 and December 2020. Manual segmentation of 121 CTAs was performed for the aortic arch, common carotid artery (CCA) and ICA. These were used to train a nnUNet. The remaining 258 CTAs were segmented using the trained nnUNet with manual verification afterwards. Angles of left and right ICAs were measured resulting in two classes: acute angle ≤ 90° and > 90°. The segmentations together with angle measurements were used to train a convolutional neural network (CNN) determining the ICA angle. The performance was evaluated using Dice scores. The classification was evaluated using AUC and accuracy. Associations of ICA angle and procedural times was explored using median and Whitney‑U test.
RESULTS: Median EVT duration for cases with ICA angle > 90° was 48 min and with ≤ 90° was 64 min (p = 0.001). Segmentation evaluation showed Dice scores of 0.94 for the aorta and 0.86 for CCA/ICA, respectively. Evaluation of ICA angle determination resulted in an AUC of 0.92 and accuracy of 0.85.
CONCLUSIONS: The association between ICA angle and EVT duration could be verified and a DL-based method for semi-automatic assessment with the potential for full automation was developed. More anatomical features of interest could be examined in a similar fashion.

UNASSIGNED: Recipient donor matching in liver transplantation can require precise estimations of liver volume. Currently utilized demographic-based organ volume estimates are imprecise and nonspecific. Manual image organ annotation from medical imaging is effective; however, this process is cumbersome, often taking an undesirable length of time to complete. Additionally, manual organ segmentation and volume measurement incurs additional direct costs to payers for either a clinician or trained technician to complete. Deep learning-based image automatic segmentation tools are well positioned to address this clinical need.
UNASSIGNED: To build a deep learning model that could accurately estimate liver volumes and create 3D organ renderings from computed tomography (CT) medical images.
UNASSIGNED: We trained a nnU-Net deep learning model to identify liver borders in images of the abdominal cavity. We used 151 publicly available CT scans. For each CT scan, a board-certified radiologist annotated the liver margins (ground truth annotations). We split our image dataset into training, validation, and test sets. We trained our nnU-Net model on these data to identify liver borders in 3D voxels and integrated these to reconstruct a total organ volume estimate.
UNASSIGNED: The nnU-Net model accurately identified the border of the liver with a mean overlap accuracy of 97.5% compared with ground truth annotations. Our calculated volume estimates achieved a mean percent error of 1.92% + 1.54% on the test set.
UNASSIGNED: Precise volume estimation of livers from CT scans is accurate using a nnU-Net deep learning architecture. Appropriately deployed, a nnU-Net algorithm is accurate and quick, making it suitable for incorporation into the pretransplant clinical decision-making workflow.